메뉴 건너뛰기




Volumn 10, Issue 2, 2014, Pages 137-147

Assessing the validity of QSARs for ready biodegradability of chemicals: An applicability domain perspective

Author keywords

Applicability domain; Biodegradability; Local centred mahalanobis distance; Model validation; QSAR

Indexed keywords

COMPUTATIONAL CHEMISTRY; MOLECULES;

EID: 84904763709     PISSN: 15734099     EISSN: 18756697     Source Type: Journal    
DOI: 10.2174/1573409910666140410110241     Document Type: Article
Times cited : (26)

References (51)
  • 1
    • 1542786165 scopus 로고    scopus 로고
    • Designing biodegradable chemicals
    • In, DeVito, S.C., Garrett, R.L., Eds.; American Chemical Society: Washington, DC
    • Boethling, R. S. Designing biodegradable chemicals. In Designing Safer Chemicals; DeVito, S. C., Garrett, R. L., Eds.; American Chemical Society: Washington, DC, 1996; Vol. 640, pp. 156-171.
    • (1996) Designing Safer Chemicals , vol.640 , pp. 156-171
    • Boethling, R.S.1
  • 2
    • 0038784757 scopus 로고    scopus 로고
    • Environmental persistence of chemicals and their carcinogenic risks to humans
    • Pollack, N.; Cunningham, A. R.; Rosenkranz, H. S. Environmental persistence of chemicals and their carcinogenic risks to humans. Mutat. Res., 2003, 528, 81-91.
    • (2003) Mutat. Res , vol.528 , pp. 81-91
    • Pollack, N.1    Cunningham, A.R.2    Rosenkranz, H.S.3
  • 3
    • 84904755753 scopus 로고    scopus 로고
    • (Accessed 28 July, 2013)
    • REACH in brief-European Commission-Europa. http://ec. europa. eu/environment/chemicals/reach/pdf/2007_02_reach_in_brief. pdf (Accessed 28 July, 2013).
    • REACH in brief-European Commission-Europa
  • 6
    • 84876578435 scopus 로고    scopus 로고
    • Quantitative structure-activity relationship models for ready biodegradability of chemicals
    • Mansouri, K.; Ringsted, T.; Ballabio, D.; Todeschini, R.; Consonni, V. Quantitative structure-activity relationship models for ready biodegradability of chemicals. J. Chem. Inf. Model., 2013, 53, 867-878.
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 867-878
    • Mansouri, K.1    Ringsted, T.2    Ballabio, D.3    Todeschini, R.4    Consonni, V.5
  • 7
    • 84861521242 scopus 로고    scopus 로고
    • Comparison of different approaches to define the applicability domain of QSAR models
    • Sahigara, F.; Mansouri, K.; Ballabio, D.; Mauri, A.; Consonni, V.; Todeschini, R. Comparison of different approaches to define the applicability domain of QSAR models. Molecules, 2012, 17, 4791-4810.
    • (2012) Molecules , vol.17 , pp. 4791-4810
    • Sahigara, F.1    Mansouri, K.2    Ballabio, D.3    Mauri, A.4    Consonni, V.5    Todeschini, R.6
  • 9
    • 8344223858 scopus 로고    scopus 로고
    • The prospects for using (Q)SARs in a changing political environment: High expectations and a key role for the European Commission's Joint Research Centre
    • Worth, A. P.; van Leeuwen, C. J.; Hartung, T. The prospects for using (Q)SARs in a changing political environment: high expectations and a key role for the European Commission's Joint Research Centre. SAR QSAR Environ. Res., 2004, 15, 331-343.
    • (2004) SAR QSAR Environ. Res , vol.15 , pp. 331-343
    • Worth, A.P.1    van Leeuwen, C.J.2    Hartung, T.3
  • 10
    • 27744520085 scopus 로고    scopus 로고
    • An approach to determining applicability domains for QSAR group contribution models: An analysis of SRC KOWWIN
    • Nikolova-Jeliazkova, N.; Jaworska, J. An approach to determining applicability domains for QSAR group contribution models: an analysis of SRC KOWWIN. Altern. Lab. Anim., 2005, 33, 461-470.
    • (2005) Altern. Lab. Anim , vol.33 , pp. 461-470
    • Nikolova-Jeliazkova, N.1    Jaworska, J.2
  • 11
    • 10044263240 scopus 로고    scopus 로고
    • Similarity to molecules in the training set is a good discriminator for prediction accuracy in QSAR
    • Sheridan, R.; Feuston, R. P.; Maiorov, V. N.; Kearsley, S. Similarity to molecules in the training set is a good discriminator for prediction accuracy in QSAR. J. Chem. Inf. Comp. Sci. 2004, 44, 1912-1928.
    • (2004) J. Chem. Inf. Comp. Sci , vol.44 , pp. 1912-1928
    • Sheridan, R.1    Feuston, R.P.2    Maiorov, V.N.3    Kearsley, S.4
  • 13
    • 84879995135 scopus 로고    scopus 로고
    • Defining a novel knearest neighbours approach to assess the applicability domain of a QSAR model for reliable predictions
    • Sahigara, F.; Ballabio, D; Todeschini, R.; Consonni, V. Defining a novel knearest neighbours approach to assess the applicability domain of a QSAR model for reliable predictions. J. Cheminformatics, 2013, 5, 27.
    • (2013) J. Cheminformatics , vol.5 , pp. 27
    • Sahigara, F.1    Ballabio, D.2    Todeschini, R.3    Consonni, V.4
  • 15
    • 84872749396 scopus 로고    scopus 로고
    • CHRIP National Institute of Technology and Evaluation (NITE) of Japan, (accessed 28 July, 2012)
    • CHRIP National Institute of Technology and Evaluation (NITE) of Japan, Chemical Risk Information Platform http://www. safe. nite. go. jp/english/kizon/KIZON_start_hazkizon. ht ml (accessed 28 July, 2012).
    • Chemical Risk Information Platform
  • 19
    • 84904718110 scopus 로고    scopus 로고
    • (accessed 28 July, 2013)
    • Environment Canada DSL (Domestic Substances List) http://www. ec. gc. ca/lcpecepa/default. asp?lang=En&n=5F213FA81&wsd oc=D031CB30-B31B-D54C-0E46-37E32D526A1F (accessed 28 July, 2013).
    • Environment Canada DSL (Domestic Substances List)
  • 21
    • 0345019845 scopus 로고    scopus 로고
    • Genetic algorithms applied to feature selection in PLS regression: How and when to use them
    • Leardi, R.; Lupianez Gonzalez, A. Genetic algorithms applied to feature selection in PLS regression: How and when to use them. Chemom. Intell. Lab. Syst., 1998, 41, 195-207.
    • (1998) Chemom. Intell. Lab. Syst , vol.41 , pp. 195-207
    • Leardi, R.1    Lupianez Gonzalez, A.2
  • 22
    • 0001757405 scopus 로고
    • The K-nearest neighbour classification rule (pattern recognition) applied to nuclear magnetic resonance spectral interpretation
    • Kowalski, B. R.; Bender, C. F. The K-nearest neighbour classification rule (pattern recognition) applied to nuclear magnetic resonance spectral interpretation. Anal. Chem., 1972, 44, 1405-1411.
    • (1972) Anal. Chem , vol.44 , pp. 1405-1411
    • Kowalski, B.R.1    Bender, C.F.2
  • 24
    • 85164278893 scopus 로고
    • Partial least squares analysis with crossvalidation for the two-class problem: A Monte Carlo study
    • Stahle, L.; Wold, S. Partial least squares analysis with crossvalidation for the two-class problem: A Monte Carlo study. J. Chemom., 1987, 1, 185-196.
    • (1987) J. Chemom , vol.1 , pp. 185-196
    • Stahle, L.1    Wold, S.2
  • 28
    • 27744590591 scopus 로고    scopus 로고
    • QSAR Applicabilty domain estimation by projection of the training set descriptor space: A review
    • Jaworska, J.; Nikolova-Jeliazkova, N.; Aldenberg, T. QSAR Applicabilty domain estimation by projection of the training set descriptor space: A review. Altern. Lab. Anim., 2005, 33, 445-459.
    • (2005) Altern. Lab. Anim , vol.33 , pp. 445-459
    • Jaworska, J.1    Nikolova-Jeliazkova, N.2    Aldenberg, T.3
  • 30
    • 54249125512 scopus 로고    scopus 로고
    • Critical assessment of QSAR models of environmental toxicity against Tetrahymena pyriformis: Focusing on applicability domain and overfitting by variable selection
    • Tetko, I. V.; Sushko, I.; Pandey, A. K.; Zhu, H.; Tropsha, A.; Papa, E.; Oberg, T.; Todeschini, R.; Fourches, D.; Varnek, A. Critical assessment of QSAR models of environmental toxicity against Tetrahymena pyriformis: Focusing on applicability domain and overfitting by variable selection. J. Chem. Inf. Model., 2008, 48, 1733-1746.
    • (2008) J. Chem. Inf. Model , vol.48 , pp. 1733-1746
    • Tetko, I.V.1    Sushko, I.2    Pandey, A.K.3    Zhu, H.4    Tropsha, A.5    Papa, E.6    Oberg, T.7    Todeschini, R.8    Fourches, D.9    Varnek, A.10
  • 33
    • 84898431324 scopus 로고
    • Variable kernel estimates of multivariate densities
    • Breiman, L.; Meisel, W.; Purcell, E. Variable kernel estimates of multivariate densities. Technometrics, 1977, 19, 135-144.
    • (1977) Technometrics , vol.19 , pp. 135-144
    • Breiman, L.1    Meisel, W.2    Purcell, E.3
  • 34
    • 84879886661 scopus 로고    scopus 로고
    • Locally centred mahalanobis distance: A new distance measure with salient features towards outlier detection
    • Todeschini, R.; Ballabio, D.; Consonni, V.; Sahigara, F.; Filzmoser, P. Locally centred mahalanobis distance: a new distance measure with salient features towards outlier detection. Anal. Chim. Acta, 2013, 787, 1-9.
    • (2013) Anal. Chim. Acta , vol.787 , pp. 1-9
    • Todeschini, R.1    Ballabio, D.2    Consonni, V.3    Sahigara, F.4    Filzmoser, P.5
  • 36
    • 84879969042 scopus 로고    scopus 로고
    • Available online, (Accessed 28 July, 2013)
    • Box plot-MATLAB. Available online: http://www. mathworks. it/it/help/stats/boxplot. html (Accessed 28 July, 2013).
    • Box plot-MATLAB
  • 37
    • 0000986928 scopus 로고
    • Degradation of halogenated and sulfonated hydrocarbons
    • (Eds), New York, NY, USA, 1982, In: Leisinger, T., Hütter, R., Cook, AM and Nüesch, J
    • Knackmuss, H.; Knackmuss, H. J. 1981. Degradation of halogenated and sulfonated hydrocarbons. In: Leisinger, T., Hütter, R., Cook, AM and Nüesch, J. (Eds), Microbial Degradation of Xenobiotics and Recalcitrant Compounds Academic, New York, NY, USA, 1982, pp. 190-212.
    • (1981) Microbial Degradation of Xenobiotics and Recalcitrant Compounds Academic , pp. 190-212
    • Knackmuss, H.1    Knackmuss, H.J.2
  • 38
    • 0035743214 scopus 로고    scopus 로고
    • Modeling lifetime and degradability of organic compounds in air, soil and water systems (IUPAC Technical Report)
    • Sabljic, A.; Peijnenburg, W. Modeling lifetime and degradability of organic compounds in air, soil and water systems (IUPAC Technical Report). Pure Appl. Chem., 2001, 73, 1331-1348.
    • (2001) Pure Appl. Chem , vol.73 , pp. 1331-1348
    • Sabljic, A.1    Peijnenburg, W.2
  • 40
    • 0009591637 scopus 로고
    • Modelling biodegradation by an example-based learning system
    • Gamberger, D.; Sekusak, S.; Sabljic, A. Modelling biodegradation by an example-based learning system. Informatica, 1993, 17, 157-166.
    • (1993) Informatica , vol.17 , pp. 157-166
    • Gamberger, D.1    Sekusak, S.2    Sabljic, A.3
  • 41
    • 0015810230 scopus 로고
    • Nonbiodegradable and other recalcitrant molecules
    • Alexander, M. Nonbiodegradable and other recalcitrant molecules. Biotechnol. Bioeng., 1973, 15, 611-647.
    • (1973) Biotechnol. Bioeng , vol.15 , pp. 611-647
    • Alexander, M.1
  • 43
    • 0006062627 scopus 로고
    • Lyman, W.J.; Reehl, W.F.; Rosenblatt, D. H, In:, (Eds.), Handbook of Chemical Property Estimation Methods: Environmental Behavior of Organic Compounds, McGraw-Hill, New York
    • Scow, K. M. Rate of biodegradation. In: Lyman, W. J.; Reehl, W. F.; Rosenblatt, D. H. (Eds.), Handbook of Chemical Property Estimation Methods: Environmental Behavior of Organic Compounds, McGraw-Hill, New York, 1982.
    • (1982) Rate of biodegradation
    • Scow, K.M.1
  • 44
    • 0033872735 scopus 로고    scopus 로고
    • Prediction for biodegradability of chemicals by an empirical flowchart
    • Hiromatsu, K.; Yakabe, Y.; Katagiri, K.; Nishihara, T. Prediction for biodegradability of chemicals by an empirical flowchart. Chemosphere, 2000, 41, 1749-1754.
    • (2000) Chemosphere , vol.41 , pp. 1749-1754
    • Hiromatsu, K.1    Yakabe, Y.2    Katagiri, K.3    Nishihara, T.4
  • 45
    • 0001941045 scopus 로고
    • Basic knowledge and perspectives on biodegradation of 2, 4, 6-trinitrotoluene and related nitroaromatic compounds in contaminated soil
    • In:, New York, NY: Plenum Press, vol. 49. ed. Spain, J.C., ISBN 0-306-45014-3
    • Rieger, P. G.; Knackmuss, H. J. Basic knowledge and perspectives on biodegradation of 2, 4, 6-trinitrotoluene and related nitroaromatic compounds in contaminated soil. In: Biodegradation of Nitroaromatic Compounds. Environmental Science Research, New York, NY: Plenum Press, 1995, vol. 49. ed. Spain, J. C. pp. 1-18., ISBN 0-306-45014-3.
    • (1995) Biodegradation of Nitroaromatic Compounds. Environmental Science Research , pp. 1-18
    • Rieger, P.G.1    Knackmuss, H.J.2
  • 46
    • 0017134307 scopus 로고
    • Microbial transformation of 2, 4, 6-trinitrotoluene and other nitroaromatic compounds
    • McCormick, N. G.; Feeherry, F. F.; Levinson, H. S. Microbial transformation of 2, 4, 6-trinitrotoluene and other nitroaromatic compounds. Appl. Environ. Microbiol., 1976, 31, 949-958.
    • (1976) Appl. Environ. Microbiol , vol.31 , pp. 949-958
    • McCormick, N.G.1    Feeherry, F.F.2    Levinson, H.S.3
  • 47
    • 3542998144 scopus 로고    scopus 로고
    • Biodegradation of nitroaromatics and other nitrogen-containing xenobiotics
    • Ye, J.; Singh, A.; Owen P. W. Biodegradation of nitroaromatics and other nitrogen-containing xenobiotics. World J. Microbiol. Biotechnol., 2000, 20, 117-135.
    • (2000) World J. Microbiol. Biotechnol , vol.20 , pp. 117-135
    • Ye, J.1    Singh, A.2    Owen, P.W.3
  • 48
    • 0014314575 scopus 로고
    • Oxidative degradation of aromatic hydrocarbons by microorganisms. I. Enzymatic formation of catechol from benzene
    • Gibson, D. T.; Koch, J. R.; Kallio, R. E. Oxidative degradation of aromatic hydrocarbons by microorganisms. I. Enzymatic formation of catechol from benzene. Biochemistry, 1968, 7, 2653-2662.
    • (1968) Biochemistry , vol.7 , pp. 2653-2662
    • Gibson, D.T.1    Koch, J.R.2    Kallio, R.E.3
  • 49
    • 0142089684 scopus 로고    scopus 로고
    • Recent developments in broadly applicable structure-biodegradability relationships
    • Jaworska, J.; Boethling R. S.; Howard, P. H. Recent developments in broadly applicable structure-biodegradability relationships. Environ. Toxicol. Chem., 2003, 22, 1710-1723.
    • (2003) Environ. Toxicol. Chem , vol.22 , pp. 1710-1723
    • Jaworska, J.1    Boethling, R.S.2    Howard, P.H.3
  • 50
    • 0005993776 scopus 로고
    • Interpreting results from biodegradability tests of chemicals in water and soil
    • Howard P. H.; Banerjee, S. Interpreting results from biodegradability tests of chemicals in water and soil. Environ. Toxicol. Chem., 1984, 3, 551-562.
    • (1984) Environ. Toxicol. Chem , vol.3 , pp. 551-562
    • Howard, P.H.1    Banerjee, S.2
  • 51


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.